title: refM03

description: pool of 10 male individuals

value: male


title: refM01

status: Public on May 28 2009

type: genomic

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: pool of 10 male individuals

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: CNAG 2.0 and Affymetrix Genotypic Console 2.1

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

tag: gender

tag: sample

value: control sample

tag: tissue

value: Peripheral blood


title: refM05

description: pool of 10 male individuals


title: UPN60_T-cell

description: FACs-sorted T-cell fraction

source_name: T-cell fraction

value: T-cell fraction

tag: disease state

value: MDS


title: UPN33_T-cell

description: FACs-sorted T-cell fraction


title: refF02

description: pool of 10 female individuals

value: female


title: UPN12_T-cell

description: FACs-sorted T-cell fraction


title: UPN103_MDS

description: primary MDS diagnosis sample

source_name: Bone marrow

value: Bone marrow


title: UPN20_T-cell

description: FACs-sorted T-cell fraction


title: UPN06_T-cell

description: FACs-sorted T-cell fraction


title: refM02

description: pool of 10 male individuals


title: UPN02_T-cell

description: FACs-sorted T-cell fraction


title: refF03

description: pool of 10 female individuals


title: refM04

description: pool of 10 male individuals


title: UPN105_MDS

description: primary MDS diagnosis sample


title: UPN106_MDS

description: primary MDS diagnosis sample


title: UPN104_MDS

description: primary MDS diagnosis sample


title: UPN102_MDS

description: primary MDS diagnosis sample


title: UPN100_MDS

description: primary MDS diagnosis sample


title: UPN34_T-cell

description: FACs-sorted T-cell fraction


title: UPN93_MDS

description: primary MDS diagnosis sample


title: UPN94_MDS

description: primary MDS diagnosis sample


title: UPN97_MDS

description: primary MDS diagnosis sample


title: UPN99_MDS

description: primary MDS diagnosis sample


title: UPN96_MDS

description: primary MDS diagnosis sample


title: UPN98_MDS

description: primary MDS diagnosis sample


title: UPN91_MDS

description: primary MDS diagnosis sample


title: UPN89_MDS

description: primary MDS diagnosis sample


title: UPN84_MDS

description: primary MDS diagnosis sample


title: UPN81_MDS

description: primary MDS diagnosis sample


title: UPN78_MDS

description: primary MDS diagnosis sample


title: UPN79_MDS

description: primary MDS diagnosis sample


title: UPN88_MDS

description: primary MDS diagnosis sample


title: UPN80_MDS

description: primary MDS diagnosis sample


title: UPN90_MDS

description: primary MDS diagnosis sample


title: UPN87_MDS

description: primary MDS diagnosis sample


title: UPN77_MDS

description: primary MDS diagnosis sample


title: UPN86_MDS

description: primary MDS diagnosis sample


title: UPN85_MDS

description: primary MDS diagnosis sample


title: UPN92_MDS

description: primary MDS diagnosis sample


title: UPN83_MDS

description: primary MDS diagnosis sample


title: UPN76_MDS

description: primary MDS diagnosis sample


title: UPN75_MDS

description: primary MDS diagnosis sample


title: UPN74_MDS

description: primary MDS diagnosis sample


title: UPN73_MDS

description: primary MDS diagnosis sample


title: UPN69_MDS

description: primary MDS diagnosis sample


title: UPN67_MDS

description: primary MDS diagnosis sample


title: UPN68_MDS

description: primary MDS diagnosis sample


title: UPN72_MDS

description: primary MDS diagnosis sample


title: UPN65_MDS

description: primary MDS diagnosis sample


title: UPN66_MDS

description: primary MDS diagnosis sample


title: UPN57_MDS

description: primary MDS diagnosis sample


title: UPN71_MDS

description: primary MDS diagnosis sample


title: UPN64_MDS

description: primary MDS diagnosis sample


title: UPN61_MDS

description: primary MDS diagnosis sample


title: UPN59_MDS

description: primary MDS diagnosis sample


title: CdLsBcell hScc1-1

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: Cohesin distribution in CdLs Bcells

hyb_protocol: Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: Array intensity data from duplicated experiments of ChIP and WCE fraction were compared by MAT (Model-based Analysis of Tiling-array) algorithm, using the software provided by the laboratory of X.Shirley Liu (http://chip.dfci.harvard.edu/~wli/MAT/). We calculated MAT score and mapped the results to genomic positions in human genome assembly hg 18 (NCBI Build 36). Bandwidth, MaxGap, and MinProbe parameters were set to 250, 1000, and 12, respectively. Cutoff threshold p-values were set to 1.0e-6. For ChIP-chip analysis, we use two IP .CEL files and two WCE .CEL files (they are duplicated experiments) to make one profile (see sample.txt file appended below).

source_name: hScc1ChIP DNA from CdLs patient Bcell

label_protocol: End labelled with biotin (biotin-11-ddATP) using Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).

extract_protocol: Cells at 70-80% confluency were crosslinked with 1% formaldehyde for 10 min and after quenching with 125 mM glycine prepared for ChIP. Genomic DNA was obtained by sonication. Chromatin immunoprecipitation was performed using hScc1 antibody. The lysate was incubated with the antibodies over night. Then the pre-absorbed protein A Affiprep beads (Bio-Rad) were added and incubated for 2 hours at 4 degree. The beads were washed several times and eluted for 20 min at 65 degree with elution buffer (50 mM Tris, 10 mM EDTA, 1 % SDS). The eluate from the beads was treated with Proteinase K and decrosslinked at 65°C over night. Contaminating RNA was removed by RNAse treatment. Then the sample was further purified by phenol-chloroform extraction and one additional purification step using the PCR purification kit (Qiagen).

treatment_protocol: Normal condition

tag: Asynchronous culture

source_name: INPUT DNA from CdLs patient Bcell


title: Bcell hScc1-1

description: Cohesin distribution in Bcells

source_name: hScc1ChIP DNA from healthy human Bcell

source_name: INPUT DNA from healthy human Bcell


title: UPN58_MDS

description: primary MDS diagnosis sample


title: UPN54_MDS

description: primary MDS diagnosis sample


title: UPN56_MDS

description: primary MDS diagnosis sample


title: UPN52_MDS

description: primary MDS diagnosis sample


title: UPN62_MDS

description: primary MDS diagnosis sample


title: UPN60_MDS

description: primary MDS diagnosis sample


title: UPN55_MDS

description: primary MDS diagnosis sample


title: UPN53_MDS

description: primary MDS diagnosis sample


title: UPN63_MDS

description: primary MDS diagnosis sample


title: UPN51_MDS

description: primary MDS diagnosis sample


title: UPN50_MDS

description: primary MDS diagnosis sample


title: UPN49_MDS

description: primary MDS diagnosis sample


title: UPN47_MDS

description: primary MDS diagnosis sample


title: UPN48_MDS

description: primary MDS diagnosis sample


title: UPN45_MDS

description: primary MDS diagnosis sample


title: mouse318_vs_female_pool: liver

status: Public on Aug 31 2009

type: RNA

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

hyb_protocol: The hybridizations were performed to single arrays (individuals F2 samples labeled with Cy5 and reference pools labeled with Cy3 fluorochromes) for 24 h in a hybridization chamber, washed, and scanned using a confocal laser scanner. Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance21 (type I error)

scan_protocol: Standard dual-channel Agilent scanner with manufacturer provided software.

data_processing: See Rosetta Error Model (PMID: 16522673)

molecule: polyA RNA

organism: Mus musculus

source_name: mouse318, liver

label_protocol: Three micrograms of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome. Labeled complementary RNA (cRNA) from each F2 animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from 150 F2 animals and parental mouse strains for each of the three tissues.

growth_protocol: All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum. Mice were fed Purina Chow until 10 wk of age, and then fed western diet (Teklad 88137, Harlan Teklad) for the subsequent 8 wk.

extract_protocol: Mouse tissues were homogenized, and total RNA extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.

treatment_protocol: Mice were fasted overnight before they were killed. Their tissues were collected, flash frozen in liquid nitrogen, and stored in −80 °C prior to RNA isolation.  All procedures of housing and treatment of animals were performed in accordance with Institutional Animal Care and Use Committee regulations.

tag: strain

value: CAST/EiJ x C57BL/6J

tag: treatment category

value: test sample

value: liver

tag: sex

source_name: reference pool (female, liver)

value: reference pool


title: UPN38_MDS

description: primary MDS diagnosis sample


title: UPN30_MDS

description: primary MDS diagnosis sample


title: UPN43_MDS

description: primary MDS diagnosis sample


title: UPN44_MDS

description: primary MDS diagnosis sample


title: UPN40_MDS

description: primary MDS diagnosis sample


title: UPN41_MDS

description: primary MDS diagnosis sample


title: UPN31_MDS

description: primary MDS diagnosis sample


title: UPN34_MDS

description: primary MDS diagnosis sample


title: UPN42_MDS

description: primary MDS diagnosis sample


title: UPN46_MDS

description: primary MDS diagnosis sample


title: UPN36_MDS

description: primary MDS diagnosis sample


title: mouse215_vs_female_pool: liver

source_name: mouse215, liver


title: UPN32_MDS

description: primary MDS diagnosis sample


title: UPN29_MDS

description: primary MDS diagnosis sample


title: UPN39_MDS

description: primary MDS diagnosis sample


title: UPN27_MDS

description: primary MDS diagnosis sample


title: UPN28_MDS

description: primary MDS diagnosis sample


title: UPN37_MDS

description: primary MDS diagnosis sample


title: CdLsBcell hScc1-2

description: Cohesin distribution in CdLs Bcells


title: Bcell hScc1-2

description: Cohesin distribution in Bcells


title: UPN25_MDS

description: primary MDS diagnosis sample


title: UPN33_MDS

description: primary MDS diagnosis sample


title: UPN22_MDS

description: primary MDS diagnosis sample


title: UPN35_MDS

description: primary MDS diagnosis sample


title: UPN26_MDS

description: primary MDS diagnosis sample


title: UPN24_MDS

description: primary MDS diagnosis sample


title: 1 hour post-stimulation 4

city: San Antonio

first: stephen

middle: e

last: harris

state: TX

address: 7703 Floyd Curl Drive

department: Periodontics

country: USA

institute: U. of Texas Health Sci Center at San Antonio

description: MC3T3 osteoblasts RNA was harvested at 1-hour as experimental samples, for comparison to the control group without dynamic fluid flow.

hyb_protocol: Labeled cDNA were hybridized to MMArray microarrays (Stanford) that represents 18,200 mouse genes in quadruplicate for both time points. Fluor was reversed in two of the replicate arrays to minimize dye-dependent bias.

scan_protocol: Arrays were scanned using Genepix 4000B scanner, and images were analyzed with Genepix Pro 5 software

data_processing: Resulting ratio data for each spot were normalized using a spatial 2D algorithm with log-linear interpolated background correction using Stanford microarray database website

molecule: total RNA

source_name: MC3T3 osteoblasts 1 hr post-oscillatory fluid flow stimulation

label_protocol: cDNA synthesized from total RNA was labeled with Cy3 and Cy5

growth_protocol: MC3T3 osteoblasts were grown in αMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37ºC

extract_protocol: Total RNA was extracted using Qiagen Rneasy kit

treatment_protocol: Oscillatory fluid flow was applied when cell density reached 80-90% confluency using a feedback-controlled fluid flow device (EnduraTec, Eden Prairie, MN). Maximum shear stress is within 10dynes/cm2 regime using a sinusoidal profile at 1Hz. The duration of flow was either 0 minutes(untreated), 30 minutes, or 1 hour.

tag: cell line

value: MC3T3 osteoblasts

tag: treatment

source_name: untreated MC3T3 osteoblasts

value: untreated


title: 1 hour post-stimulation 3

value: 1 hr post-oscillatory fluid flow stimulation


title: UPN23_MDS

description: primary MDS diagnosis sample


title: 30 min post-stimulation 4

description: MC3T3 osteoblasts RNA was harvested at 30-minute as experimental samples, for comparison to the control group without dynamic fluid flow.

source_name: MC3T3 osteoblasts 30 min post-oscillatory fluid flow stimulation


title: 1 hour post-stimulation 2


title: 30 min post-stimulation 2

value: 30 min post-oscillatory fluid flow stimulation


title: 1 hour post-stimulation 1


title: UPN19_MDS

description: primary MDS diagnosis sample


title: LNCaP siART-27 plus R1881, rep2

city: New York

first: Susan

last: Logan

state: NY

address: 550 First Ave., MSB 249

institute: NYU School of Medicine

description: Transfected with 100 nM Dharmacon siRNAs using Lipofectamine 2000 reagent (Invitrogen).

hyb_protocol: Total RNA was hybridized at the Memorial Sloan-Kettering genomics core facility.

scan_protocol: Total RNA was scanned at the Memorial Sloan-Kettering genomics core facility.

data_processing: RMA normalization (1. Per chip: normalize to 50th percentile and 2. Per Gene: normalize to naive samples siCTRL_ETOH_1 and _2) was performed and androgen-regulated genes in each cellular context were determined as previously described using Genespring software (Agilent Technologies, Santa Clara, CA) and a 2-fold change threshold.

source_name: LNCaP cells, siART-27, R1881, 18 hrs

label_protocol: Total RNA was labeled at the Memorial Sloan-Kettering genomics core facility.

growth_protocol: LNCaP cells were cultured in RPMI-1640 media (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT) and 1% penicillin-streptomycin (Mediatech/ Cellgro, Henrdon, VA). The cells were maintained at 5% CO2 in a 37oC incubator.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini kit (Qiagen Inc., Valencia, CA) according to manufacturer's protocol.

treatment_protocol: Non-silencing (control) and ART-27 (SMARTpool) siRNA were purchased from Dharmacon (Lafayette, CO). LNCaP cells incubated overnight in cs media were transfected in Opti-MEM media (Invitrogen) using 100 nM of each siRNA, and Lipofectamine 2000 (Invitrogen) according to manufacturer’s protocol. After 4 h, the cells were allowed to recover overnight in cs media. The cells were then treated with ethanol vehicle or 10 nM R1881 for 18 hrs.

tag: Gender

tag: Tissue

value: Prostate Cancer, Epithelial


title: 30 min post-stimulation 1


title: LNCaP siART-27 plus R1881, rep1


title: UPN20_MDS

description: primary MDS diagnosis sample


title: UPN16_MDS

description: primary MDS diagnosis sample


title: UPN14_MDS

description: primary MDS diagnosis sample


title: LNCaP siART-27 plus ethanol, rep1

source_name: LNCaP cells, siART-27, Ethanol Veh, 18 hrs


title: LNCaP siART-27 plus ethanol, rep2


title: LNCaP control plus R1881, rep2

source_name: LNCaP cells, siControl, R1881, 18 hrs


title: UPN17_MDS

description: primary MDS diagnosis sample


title: 30 min post-stimulation 3


title: UPN11_MDS

description: primary MDS diagnosis sample


title: UPN13_MDS

description: primary MDS diagnosis sample


title: UPN09_MDS

description: primary MDS diagnosis sample


title: UPN18_MDS

description: primary MDS diagnosis sample


title: LNCaP control plus R1881, rep1


title: UPN15_MDS

description: primary MDS diagnosis sample


title: MCF-7 cells_NMNAT1 knockdown_E2_replicate 3

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: Standard hybridization to Affymetrix U133A 2.0 microarray

scan_protocol: Standard scanning protocol using GeneChip Scanner

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling.  Signals were subsequently normalized through the following steps: common probe sets on both U133 A2.0 and U133 Plus2.0 platforms were selected; within each sample group hybridized to the same microarray platform, the signal values were log2 transformed, median centered for the array, and median centered for each gene; the data sets were further adjusted using the parametric empirical Bayes method (Combat R).

label: Biotin

source_name: MCF-7 cells, NMNAT1 knockdown, E2 treatment 3 hours

label_protocol: Seven µg of total RNA were subjected to One-cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray

growth_protocol: MCF-7 cells were maintained in Eagle's minimum essential medium supplemented with 5% calf serum and antibiotics.

extract_protocol: Total RNA was prepared using Trizol reagent according to the manufacturer's instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen)

treatment_protocol: MCF-7 cells were cultured in estrogen-free media for 72 hours prior to hormone treatment. E2 samples were treated with 10-7M estradiol for 3 hours.


title: Th17 cells 2

city: Seattle

first: Qiang

last: Tian

state: WA

institute: Institute for Systems Biology

description:
OT-II Tcr transgenic mice on C57BL/6 background, OT-II peptide and APC, age 6-8 weeks, spleen and limph node CD4 T cells, Th17
Naïve CD4 T cells were activated with OT-II peptide and APC under Th17 conditions for 5 days

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were GCRMA normalized using R/Bioconductor

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

growth_protocol: Cells were cultured in RPMI-1640 medium containing 10% FBS, 1 % L-Glu and 1% Penicillin/streptomycin

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions.

treatment_protocol: the cytokine stimuli for Th17 differentiation were 20 ng/ml of IL-6, 5 mg/ml TGFb and 10 mg/ml of anti-IL-4 and 10 mg/ml of anti-IFNg

tag: cell type

value: Th17 cells


title: UPN12_MDS

description: primary MDS diagnosis sample

value: male


title: LNCaP control plus ethanol, rep1

source_name: LNCaP cells, siControl, Ethanol Veh, 18 hrs


title: UPN07_MDS

description: primary MDS diagnosis sample


title: MCF-7 cells_NMNAT1 knockdown_control_replicate 3

source_name: MCF-7 cells, NMNAT1 knockdown, no E2 treatment

treatment_protocol: MCF-7 cells were cultured in estrogen-free media for 72 hours prior to hormone treatment. Control cells were treated with vehicle (ethanol) for 3 hours.


title: Th2 cells 2

description:
OT-II Tcr transgenic mice on C57BL/6 background, OT-II peptide and APC, age 6-8 weeks, spleen and limph node CD4 T cells, Th2
Naïve CD4 T cells were activated with OT-II peptide and APC under Th2 conditions for 5 days

treatment_protocol: the cytokine stimuli for Th2 differentiation were 10 ng/ml of IL-4, 10 mg/ml of anti-IFNg

value: Th2 cells


title: MCF-7 cells_NMNAT1 knockdown_E2_replicate 1

tag: MCF-7 cells, NMNAT1 knockdown, E2 treatment 3 hours


title: UPN06_MDS

description: primary MDS diagnosis sample

source_name: Bone marrow


title: LNCaP control plus ethanol, rep2


title: UPN08_MDS

description: primary MDS diagnosis sample


title: UPN10_MDS

description: primary MDS diagnosis sample


title: TBP ChIP rep3

city: Lexington

first: hongyan

last: xing

state: KY

address: 741 S. Limestone

department: Biochemistry

institute: University of Kentucky

description: TBP ChIP-chip in mitosis jurkat cells

hyb_protocol: Human tiling 2.0 R C was hybridized for 16hr, washing and stained with streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the stardard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix Scanner 3000 G7.

data_processing: TAS (affymetrix) is used for data analysis.

source_name: TBP ChIP in mitotic Jurkat

label_protocol: ChIP/input  DNA was labeled by TdT with biotin following by affymetrix protocol.

growth_protocol: Jourat cell at 37C with 5% CO2 in RPMI1640 supplemented with 10% fetal calf serum (FCS), and 50µg/ml gentamycin.

extract_protocol: ChIP/input  DNA was acquired accirding to affymetrix protocol.

treatment_protocol: Enrichment of M-phase populations of cells was obtained by incubating asynchronous populations with 100ng/ml nocodazole for 16hr.

tag: polyclonal antibody for TBP


title: MCF-7 cells_NMNAT1 knockdown_control_replicate 1

tag: MCF-7 cells, NMNAT1 knockdown, no E2 treatment


title: UPN21_MDS

description: primary MDS diagnosis sample


title: Th2 cells 1

source_name: Naïve CD4 T cells were activated with OT-II peptide and APC under Th2 conditions for 5 days


title: MCF-7 cells_luciferase knockdown_E2_replicate 3

source_name: MCF-7 cells, luciferase knockdown, E2 treatment 3 hours


title: MCF-7 cells_luciferase knockdown_control_replicate 3

source_name: MCF-7 cells, luciferase knockdown, no E2 treatment


title: Th1 cells 2

description:
OT-II Tcr transgenic mice on C57BL/6 background, OT-II peptide and APC, age 6-8 weeks, spleen and limph node CD4 T cells, Th1
Naïve CD4 T cells were activated with OT-II peptide and APC under Th1 conditions for 5 days

treatment_protocol: the cytokine stimuli for Th1 differentiation were 10 ng/ml of IL-12, 10 mg/ml of anti-IL-4

value: Th1 cells


title: CdLsBcell hScc1-7

description: Cohesin distribution in CdLs Bcells

source_name: hScc1ChIP DNA from CdLs patient Bcell

source_name: INPUT DNA from CdLs patient Bcell


title: Th17 cells 1

source_name: Naïve CD4 T cells were activated with OT-II peptide and APC under Th17 conditions for 5 days


title: UPN05_MDS

description: primary MDS diagnosis sample


title: Bcell hScc1-7

description: Cohesin distribution in Bcells

source_name: hScc1ChIP DNA from healthy human Bcell

source_name: INPUT DNA from healthy human Bcell


title: MCF-7 cells_luciferase knockdown_control_replicate 1

tag: MCF-7 cells, luciferase knockdown, no E2 treatment


title: Input  rep3

description: Input DNA-chip in mitosis Jurkat cells

source_name: Input DNA in mitotic jurkat

tag: input DNA


title: TBP ChIP rep2

description: TBP ChIP-chip in mitosis jurkat cells


title: CdLsBcell hScc1-6

description: Cohesin distribution in CdLs Bcells


title: Bcell hScc1-6

description: Cohesin distribution in Bcells


title: UPN02_MDS

description: primary MDS diagnosis sample

tag: gender


title: Bcell hScc1-5

description: Cohesin distribution in Bcells


title: CdLsBcell hScc1-5

description: Cohesin distribution in CdLs Bcells


title: Input  rep1

description: Input DNA-chip in mitosis Jurkat cells


title: CdLsBcell hScc1-4

description: Cohesin distribution in CdLs Bcells


title: Input  rep2

description: Input DNA-chip in mitosis Jurkat cells


title: TBP ChIP rep1

description: TBP ChIP-chip mitosis jurkat cells


title: MCF-7 cells_NAMPT knockdown_replicate 2

description: MCF-7 cells_NAMPT knockdown_replicate 2

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling.  Signals were then log2 transformed, median centered for the array, and  median centered for each gene.

source_name: MCF-7 cells NAMPT knockdown

tag: MCF-7 cells NAMPT knockdown


title: Bcell hScc1-4

description: Cohesin distribution in Bcells


title: CdLsBcell hScc1-3

description: Cohesin distribution in CdLs Bcells


title: Bcell hScc1-3

description: Cohesin distribution in Bcells


title: MCF-7 cells_NAMPT knockdown_replicate 3

description: MCF-7 cells_NAMPT knockdown_replicate 3


title: UPN03_MDS

description: primary MDS diagnosis sample

tag: tissue

tag: disease state


title: Th1 cells 1

source_name: Naïve CD4 T cells were activated with OT-II peptide and APC under Th1 conditions for 5 days

tag: strain


title: MCF-7 cells_luciferase matching NAMPT_replicate 2

source_name: MCF-7 cells luciferase knockdown (control)


title: MCF-7 cells_NAMPT knockdown_replicate 1

description: MCF-7 cells_NAMPT knockdown_replicate 1


title: MCF-7 SIRT1 Replicate 2

hyb_protocol: Standard hybridization to Affymetrix U133A 2.0 microarray.

scan_protocol: Standard scanning protocol using GeneChip Scanner.

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling. Signals were then used in further analysis, namely batch effect adjusted and log2 median-normalized using COMBAT R.

source_name: MCF-7 SIRT1 Replicate 2

label_protocol: Seven μg of total RNA were subjected to One-Cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray.

extract_protocol: Total RNA was prepared using Trizol Reagent according to the manufacturer’s instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen).

tag: MCF-7 SIRT1 Replicate 2


title: MCF-7 cells_luciferase matching NAMPT_replicate 1

tag: MCF-7 cells luciferase knockdown (control)


title: MCF-7 cells_luciferase matching NAMPT_replicate 3


title: MCF-7 SIRT1 Replicate 3

source_name: MCF-7 SIRT1 Replicate 3

tag: MCF-7 SIRT1 Replicate 3


title: MCF-7 SIRT1 Replicate 1

source_name: MCF-7 SIRT1 Replicate 1

tag: MCF-7 SIRT1 Replicate 1


title: MCF-7 Luciferase Replicate 2

source_name: MCF-7 Cells Luciferase Knockdown (control)


title: MCF-7 Luciferase Replicate 3

tag: MCF-7 Cells Luciferase Knockdown (control)


title: MCF-7 Luciferase Replicate 1


title: 1 day treatment with Cadmium  (5F137)

status: Public on May 27 2009

city: Tel Aviv

first: yaron

last: kinar

address: 72 Pinchas Rosen st.

country: Israel

institute: Compugen

description: Gene expression data from kidneys of rats treated with Cadmium for 1 days

hyb_protocol: Performed according to the standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: Homogenized apical parts of right and left rat kidneys

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Sprague-Dawley Crl:CD(SD) rats (males and females)  were purchased from Charles River Hungary Ltd., at an approximate age of 7-8 weeks. Animals were acclimated for 6 days, and housed individually.

extract_protocol: At autopsy, both kidneys of each animal were removed and each kidney was cross sectioned. The kidney sections for the RNA analysis were homogenized using TRI reagent (MRC) and RNA was extracted following the manufacture protocol. After precipitation with isopropanol, the RNA pellet was washed with ethanol and the pellet was then resuspended in DEPC water. For further purification, the RNA was added to an equal volume of phenol:chlorophorm:isoamyl  alcohol mix (25:241:) and extracted using the MaXtract tubes (QIAGEN), following the manufacture protocol. RNA was then quantified by spectrophotometry. The quality of the RNA was evaluated by measuring the 260/280 and 260/230 ratios and confirmed by agarose gel. RNA was deemed of a suitable quality for microarray analysis if the 260/280 ratio was between 1.8 and 2.1, the 260/230 ratio was higher than 1.5 and the gel showed no visible degradation products lower than the 18S ribosomal band

treatment_protocol: untreated

value: Kidneys (apical parts)

tag: genotype

value: Sprague-Dawley

tag: age

value: 7-8 weeks as experiments starts

value: Female


title: Naive  (8F182)

description: Gene expression data from kidneys of untreated rats

scan_protocol: Performed according to the standard Affymetrix protocol


title: 5 days treatment with Gentamycin  (2F114)

description: Gene expression data from kidneys of rats treated with Gentamycin for 5 days


title: Naive  (8M82)

value: Male


title: UPN01_MDS

description: primary MDS diagnosis sample

source_name: Bone marrow

value: female

value: Bone marrow

value: MDS


title: Naive  (8M83)


title: Naive  (8F181)


title: UPN04_MDS

description: primary MDS diagnosis sample


title: Naive  (8M81)


title: 5 days treatment with Cadmium  (5M40)

description: Gene expression data from kidneys of rats treated with Cadmium for 5 days

treatment_protocol: 5 days treatment with Cadmium


title: 1 day treatment with Cisplatin  (3F120)

description: Gene expression data from kidneys of rats treated with Cisplatin for 1 days

treatment_protocol: 1 day treatment with Cisplatin


title: 5 days treatment with Cisplatin  (3M23)

description: Gene expression data from kidneys of rats treated with Cisplatin for 5 days

treatment_protocol: 5 days treatment with Cisplatin


title: 1 day treatment with Cadmium  (5M37)

treatment_protocol: 1 day treatment with Cadmium


title: 5 days treatment with Cadmium  (5F140)


title: 1 day treatment with Cadmium  (5M39)


title: 5 days treatment with Doxorubicin  (6M50)

description: Gene expression data from kidneys of rats treated with Doxorubicin for 5 days

treatment_protocol: 5 days treatment with Doxorubicin


title: 1 day treatment with Cisplatin  (3F121)


title: 5 days treatment with Doxorubicin  (6F149)


title: 5 days treatment with Tobramycin  (4F131)

description: Gene expression data from kidneys of rats treated with Tobramycin for 5 days

treatment_protocol: 5 days treatment with Tobramycin


title: 5 days treatment with Saline  (1F106)

description: Gene expression data from kidneys of rats treated with Saline for 5 days

treatment_protocol: 5 days treatment with Saline


title: 1 day treatment with Tobramycin  (4F128)

description: Gene expression data from kidneys of rats treated with Tobramycin for 1 days

treatment_protocol: 1 day treatment with Tobramycin


title: Naive  (8F183)


title: 1 day treatment with Doxorubicin  (6F148)

description: Gene expression data from kidneys of rats treated with Doxorubicin for 1 days

treatment_protocol: 1 day treatment with Doxorubicin


title: 5 days treatment with ValproicAcid  (7M60)

description: Gene expression data from kidneys of rats treated with ValproicAcid for 5 days

treatment_protocol: 5 days treatment with ValproicAcid


title: 1 day treatment with Doxorubicin  (6M46)


title: 5 days treatment with ValproicAcid  (7M59)


title: 5 days treatment with Cisplatin  (3F123)


title: 5 days treatment with Gentamycin  (2M14)

treatment_protocol: 5 days treatment with Gentamycin


title: 5 days treatment with Gentamycin  (2F113)


title: 1 day treatment with Gentamycin  (2F111)

description: Gene expression data from kidneys of rats treated with Gentamycin for 1 days

treatment_protocol: 1 day treatment with Gentamycin


title: 1 day treatment with Saline  (1F103)

description: Gene expression data from kidneys of rats treated with Saline for 1 days

treatment_protocol: 1 day treatment with Saline


title: 5 days treatment with Gentamycin  (2M13)


title: 17-DMAG(500nM)_TaY_1

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

description: 17AAG and 17DMAG are Hsp90 inhibitors.

hyb_protocol: Hybridization was carried out automatically using GeneTAC Hybstation (Genomic Solutions, US) according to the supplier’s instruction. The conditions of hybridization were 55oC for 2 hours, 50oC for 2 hours, and 46oC for 2 hours, then 42oC for 12 hours.

scan_protocol: The hybridized signals were scanned by GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA).

data_processing: The scanned data was normalized, verified, and analyzed using the Genomic Profiler software (Mitsui Industrial Knowledge, Inc, Tokyo, Japan:http://bio.mki.co.jp/en/product/index.html).

source_name: 17DMAG treated ATL cells

label_protocol: 20 microgram of RNA were labeled using a LabelStar Array kit (Qiagen) , according to the supplier’s instruction.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Germantown, MD, USA).The amount of RNA was measured by NanoDrop (NanoDrop Technologies, Wilmington, DE, USA), then the quality of extracted RNA was checked using a 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: 500nM of 17DMAG for 24 hrs

tag: Adult T-cell leukemia cell line treated with 17DMAG

source_name: TaY(Mock)

tag: TaY(Mock)


title: 17-DMAG(500nM)_TaY_2

description: 17AAG and 17DMAG are Hsp90 inhibitors.


title: 1 day treatment with Tobramycin  (4M28)


title: 1 day treatment with Gentamycin  (2M12)


title: 17-DMAG(150nM)_TaY_2

description: 17AAG and 17DMAG are Hsp90 inhibitors.

treatment_protocol: 150nM of 17DMAG for 24 hrs


title: 1 day treatment with Cisplatin  (3M20)


title: 1 day treatment with Saline  (1F101)


title: 5 days treatment with Cadmium  (5F141)


title: 5 days treatment with ValproicAcid  (7F158)


title: 5 days treatment with Saline  (1M6)


title: 5 days treatment with Tobramycin  (4M33)


title: 5 days treatment with Gentamycin  (2F115)


title: 1 day treatment with Tobramycin  (4F130)


title: 5 days treatment with Cisplatin  (3M24)


title: 1 day treatment with ValproicAcid  (7M57)

description: Gene expression data from kidneys of rats treated with ValproicAcid for 1 days

treatment_protocol: 1 day treatment with ValproicAcid


title: 5 days treatment with Cadmium  (5F142)


title: 5 days treatment with Doxorubicin  (6M49)


title: 1 day treatment with Cadmium  (5F139)


title: 17-DMAG(150nM)_TaY_1

description: 17AAG and 17DMAG are Hsp90 inhibitors.


title: MCF-7 cells_luciferase knockdown_E2_replicate 1

source_name: MCF-7 cells, luciferase knockdown, E2 treatment 3 hours

treatment_protocol: MCF-7 cells were cultured in estrogen-free media for 72 hours prior to hormone treatment. E2 samples were treated with 10-7M estradiol for 3 hours.


title: 17-DMAG(50nM)_TaY_2

description: 17AAG and 17DMAG are Hsp90 inhibitors.

treatment_protocol: 50nM of 17DMAG for 24 hrs


title: 17-DMAG(50nM)_TaY_1

description: 17AAG and 17DMAG are Hsp90 inhibitors.


title: 17-AAG(500nM)_TaY_2

description: 17AAG and 17DMAG is Hsp90 inhibitors.

source_name: 17AAG treated ATL cells

treatment_protocol: 500nM of 17AAG for 24 hrs.

tag: Adult T-cell leukemia cell line treated with 17AAG


title: 17-AAG(500nM)_TaY_1

description: 17AAG and 17DMAG are Hsp90 inhibitors.


title: 17-AAG(300nM)_TaY_1

description: 17AAG and 17DMAG are Hsp90 inhibitors.

treatment_protocol: 300nM of 17AAG for 24 hrs.


title: 17-AAG(300nM)_TaY_2

description: 17AAG and 17DMAG are Hsp90 inhibitors.


title: 5 days treatment with Doxorubicin  (6F150)


title: 5 days treatment with Saline  (1M5)


title: 5 days treatment with Cadmium  (5M42)

treatment_protocol: 5 days treatment with Cadmium


title: 17-AAG(50nM)_TaY_2

description: 17AAG and 17DMAG are Hsp90 inhibitors.


title: 1 day treatment with ValproicAcid  (7M56)


title: UPN44S_T-cell

description: FACs-sorted T-cell fraction

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA ((Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix scanner 3000.

source_name: T-cell fraction

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix).

value: T-cell fraction


title: 17-AAG(50nM)_TaY_1

description: 17AAG and 17DMAG are Hsp90 inhibitors.

treatment_protocol: 50 nM of 17AAG for 24 hrs.


title: 1 day treatment with Tobramycin  (4M30)


title: 1 day treatment with ValproicAcid  (7F157)


title: 1 day treatment with Cisplatin  (3F119)

treatment_protocol: 1 day treatment with Cisplatin


title: 5 days treatment with Cisplatin  (3F122)

treatment_protocol: 5 days treatment with Cisplatin


title: 1 day treatment with Gentamycin  (2M11)


title: 5 days treatment with Tobramycin  (4F133)

treatment_protocol: 5 days treatment with Tobramycin


title: Testis_H139

city: Chiba

first: Mitsuru

last: Nenoi

address: 4-9-1, Anagawa, Inage-ku

department: Research Center for Radiation Protection

institute: National institute of Radiological Sciences

description: Sample identifier: M12 H139

hyb_protocol: Illumina Gene Expression system Hyb E1 and Block Buffer kit, Wash E1BC Buffer kit and High Temp Wash Buffer kit

scan_protocol: Standard of BeadStation 500GX-WG system (Illumina)

source_name: irradiated mouse testis_13 μGy/min (8000 mGy)

label_protocol: Illumina RNA Amplification Kit (Label with biotin-UTP directly)

extract_protocol: RNAlater and RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Valencia, CA)

treatment_protocol: Irradiation with 137Cs γ-rays was carried out in a facility at the Institute for Environmental Sciences for 485 days (22 h/day) at dose-rates of 0.032 μGy/min, 0.65 μGy/min, and 13 μGy/min. The total dose after irradiation at these dose-rates was 21 mGy, 420 mGy, and 8000 mGy. We examined 12 mice (3 per each dose-rate condition, including the control). Mice were euthanized immediately after the termination of irradiation, and the kidney and testis were removed and stored at -80°C in RNAlater (Ambion).

tag: Male specific pathogen free C57BL/6J


title: 1 day treatment with Doxorubicin  (6F147)

treatment_protocol: 1 day treatment with Doxorubicin


title: UPN44S_MDS

description: primary MDS diagnosis sample

value: mononuclear MDS fraction


title: Testis_H134

description: Sample identifier: M11 H134


title: 5 days treatment with Cadmium  (5M41)


title: 1 day treatment with Gentamycin  (2F110)


title: Testis_M130

description: Sample identifier: M09 M130

source_name: irradiated mouse testis_0.65 μGy/min (420 mGy)


title: 1 day treatment with ValproicAcid  (7F155)


title: Testis_H132

description: Sample identifier: M10 H132


title: 1 day treatment with Doxorubicin  (6M47)


title: 5 days treatment with Saline  (1F105)

treatment_protocol: 5 days treatment with Saline


title: 1 day treatment with Doxorubicin  (6M48)


title: Testis_L117

description: Sample identifier: M04 L117

source_name: irradiated mouse testis_0.032 μGy/min (21 mGy)


title: 1 day treatment with Saline  (1M3)


title: 5 days treatment with ValproicAcid  (7F160)

treatment_protocol: 5 days treatment with ValproicAcid


title: 1 day treatment with Cadmium  (5F138)

treatment_protocol: 1 day treatment with Cadmium


title: 5 days treatment with Cisplatin  (3F124)


title: 1 day treatment with Tobramycin  (4F129)

treatment_protocol: 1 day treatment with Tobramycin


title: Testis_L119

description: Sample identifier: M06 L119


title: Testis_C109

description: Sample identifier: M02 C109

source_name: control mouse testis


title: 5 days treatment with Tobramycin  (4M31)


title: 5 days treatment with ValproicAcid  (7M58)


title: Testis_M125

description: Sample identifier: M07 M125


title: Testis_L118

description: Sample identifier: M05 L118


title: 1 day treatment with Tobramycin  (4M29)


title: 5 days treatment with Tobramycin  (4M32)


title: Testis_C110

description: Sample identifier: M03 C110


title: Testis_M129

description: Sample identifier: M08 M129


title: 5 days treatment with Doxorubicin  (6F151)

treatment_protocol: 5 days treatment with Doxorubicin


title: 1 day treatment with Doxorubicin  (6F146)


title: Testis_C102

description: Sample identifier: M01 C102


title: 5 days treatment with Tobramycin  (4F132)


title: 1 day treatment with Saline  (1M2)


title: 5 days treatment with Saline  (1M4)


title: 1 day treatment with Cisplatin  (3M21)


title: Kidney_M4

description: Sample identifier: K-400-4

source_name: irradiated mouse kidney_0.65 μGy/min (420 mGy)


title: 5 days treatment with ValproicAcid  (7F159)


title: 1 day treatment with Gentamycin  (2F112)

treatment_protocol: 1 day treatment with Gentamycin


title: Kidney_H2

description: Sample identifier: K-8000-2

source_name: irradiated mouse kidney_13 μGy/min (8000mGy)


title: Kidney_H3

description: Sample identifier: K-8000-3


title: 1 day treatment with ValproicAcid  (7F156)

treatment_protocol: 1 day treatment with ValproicAcid


title: 1 day treatment with Saline  (1F104)


title: 5 days treatment with Cisplatin  (3M22)


title: 1 day treatment with Saline  (1F102)

treatment_protocol: 1 day treatment with Saline


title: 1 day treatment with Cadmium  (5M38)


title: 5 days treatment with Gentamycin  (2M15)

treatment_protocol: 5 days treatment with Gentamycin


title: 1 day treatment with Cisplatin  (3M19)


title: Kidney_C4

description: Sample identifier: K-0-4

source_name: control mouse kidney


title: Kidney_L3

description: Sample identifier: K-20-3

source_name: irradiated mouse kidney_0.032 μGy/min (21 mGy)


title: 1 day treatment with Gentamycin  (2M10)


title: Kidney_M3

description: Sample identifier: K-400-3


title: Kidney_L4

description: Sample identifier: K-20-4


title: Kidney_H1

description: Sample identifier: K-8000-1


title: Kidney_M1

description: Sample identifier: K-400-1


title: Kidney_C3

description: Sample identifier: K-0-3


title: Kidney_L2

description: Sample identifier: K-20-2


title: 1 day treatment with ValproicAcid  (7M55)


title: 1 day treatment with Saline  (1M1)


title: 3T3-L1 day 7

status: Public on May 26 2009

type: other

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: total miRNA profiling by array

hyb_protocol: labeled miRNA was hybridized to custom arrays at 42 degrees celcius for 12h.

scan_protocol: images were scaned according to standard UTSW microarray core facility protocols.

data_processing:
Scanned images were processed using GenePix software.
The normalized signal represents the data after Lowess normalization, ratio computation (Cy5/Cy3), and log2 transformation of raw data
The term raw signal values refer to the linear data after thresholding to 1.0 and summarization for the individual channels (Cy3 and Cy5).  Summarization was performed by computing the geometric mean of replicate spots.

molecule: other

source_name: 3T3-L1 cells prior to induction of adipocyte differentiation (day 0)

label_protocol: miRNA labeling was carried out according to directions from the Ambion mirVana™ miRNA Labeling Kit.  Briefly, 1mg of extracted miRNA was appended with amine-NTPs at 37 degrees celcius for 2 hrs.  Samples were washed to remove free NTPs.  Cy3 and Cy5-NHS ester dye was coupled to amine modified miRNA at room temperature for 1hr in the dark.  Samples were washed to remove free dye.  Labeled samples were imediately used for array hybridization.  The common day 0 reference was labeled with Cy3, and days 1, 4, and 7 were labeled with Cy5.

growth_protocol: 3T3-L1 cells were cultured in a 5% CO2 humidified atmosphere in Dulbecco's Modified Eagle's Medium (DMEM)/high glucose with L-glutamine supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin, and 100mg/ml streptomycin.

extract_protocol: The standard phenol/chloroform extraction protocol was used to isolate total RNA.  MicroRNAs were isolated from total RNA using a FlashPAGE fractionator (Ambion, TX). 100mg of total RNA was loaded onto FlashPAGE precast gels and small size RNAs collected after electrophoresis at 80V for 12 minutes. Small size RNA was purified using the FlashPAGE Reaction Clean Up Kit (Ambion, TX).

treatment_protocol: For DMI induction, 1mM Dexamethasone, 0.5mM IBMX, and 5mg/ml Insulin were added to culture medium two days after the cells reached confluence. After 48 hours, the culture medium was replaced with DMEM containing 10% FBS and 5mg/ml Insulin. The same medium was replaced every 48 hours until pre-adipocytes differentiated into mature adipocytes.

tag: agent

value: untreated (control)

source_name: 3T3-L1 cells, 7 day following induction of adipocyte differentiation with  DMI cocktail

value: DMI cocktail (1mM Dexamethasone, 0.5mM IBMX, and 5mg/ml Insulin)

tag: time

value: 7 day


title: 3T3-L1 day 1

description: total miRNA profiling by array

source_name: 3T3-L1 cells, 1 day following induction of adipocyte differentiation with  DMI cocktail

value: 1 day


title: Kidney_C2

description: Sample identifier: K-0-2


title: 3T3-L1 day 4

description: total miRNA profiling by array

source_name: 3T3-L1 cells, 4 day following induction of adipocyte differentiation with  DMI cocktail

value: 4 day


title: WCE fraction of rad53 siz2 mutant treated with HU, input

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

institute: Kazusa DNA Research Institute

description:
WCE fraction of rad53 siz2 mutant treated with HU (chromosome III, IV, V, and the right arm of chromosome VI)
WCE fraction used for the nomalization of ChIP fraction
Baseline for rad53 siz2 mutant treated with HU

hyb_protocol: Following denaturation at 99 C for 10 minutes, cooling on ice, and spin-down. 200 micro liter of hybridization mixture was hybridized for 16 hours at 42 C on GeneChip SC3456a520015F using hybridization oven 640 (affymetrix). Each hybridization mixture contains the end-labbeled DNA, 6xSSPE, 0.005% Triton X-100, 0.1 mg/ml herring sperm DNA, oligo B2 (affymetrix) and hybridization control (affymetrix).

scan_protocol: Washing and scanning protocol (EukGE-WS1v3) provided by Affymetrix was performed automatically on an Affymetrix Fluidics station 400. Array was scanned by GeneChip Scanner 3000 7G.

data_processing:
Data analysis was performed as previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol.409,chapter 23,389-410 in “DNA Repair” (edited by J.Campbell) (2006).
Primary data analysis was carried out with GeneChip Operating Software (GCOS 1.4) using default settings to obtain signal and detection p-value.

organism: Saccharomyces cerevisiae

source_name: Fragmented whole genomic DNA

label_protocol: End labeling by terminal transferase

growth_protocol: Cells were grown to early log phase.

extract_protocol:
Cells were suspended in lysis buffer 140 (0.1% sodium deoxycholate, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 50 mM HEPES-KOH, pH7.5) and disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments.
1% of the WCE was used for a preparation of WCE fraction DNA (input DNA).
WCE fraction was incubated overnight at 37C with proteinase K, incubated for 6 hours at 65C, extracted with phenol/chloroform/isoamylalcohol, precipitated, and resuspended in 100 ul of 10 mM Tris-Cl (pH7.6) and incubated with RNaseA.
The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, nature). The amplified DNA was digested with Dnase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.

treatment_protocol:
Early log phase culture was harvested and resuspended in YPAD medium at 1x10e7. Then, cells were treated with 15 ug/ml alpha-factor. After confirmation of G1 arrest, alpha-factor was washed away, and the cells were incubated in YPAD containing 0.2 M HU for 90 min.
1x10e9 cells were fixed in 1% formaldehyde for 10 min at room temperature and then treated with 125 mM glycine for 5 min at room temperature. The cells were washed with 20 ml of ice-cold TBS twice, freezed with liquid nitrogen, and stored at -80C.

value: rad53 siz2 mutant expressing Rad52-13myc

tag: background

value: CY2034 R52-Myc siz2

tag: culture

value: released from G1 arrest and treated with 0.2 M HU for 90 min


title: rad53 siz2 mutant treated with HU, IP fraction

description:
Distribution of Rad52-myc on chromosome III, IV, V, and the right arm of chromosome VI (rad53 siz2 mutant treated with HU)
IP fraction used for the mapping of Rad52-13myc on chromosomes
Used baseline: WCE fraction of rad53 siz2 mutant treated with HU

data_processing:
Data analysis was performed as previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol.409,chapter 23,389-410 in “DNA Repair” (edited by J.Campbell) (2006).
Primary data analysis was carried out with GeneChip Operating Software (GCOS 1.4) using default settings to obtain signal and detection p-value.
Signals from the ChIP fraction scan were compared to the WCE fraction scan with GCOS 1.4 using default settings.

source_name: Chromatin-immunoprecipitated DNA

extract_protocol:
Cells were suspended in lysis buffer 140 (0.1% sodium deoxycholate, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 50 mM HEPES-KOH, pH7.5) and disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments.
WCE was immunoprecipitated with anti-c-Myc (9E10) antibody sc-40 (Invitrogen) coupled to protein A Dynabeads (Invitrogen).
Chromatin immunoprecipitated sample was incubated overnight at 37C with proteinase K, incubated for 6 hrs at 65C, extracted with phenol/chloroform/isoamylalcohol, precipitated, and resuspended in 10 ul of 10 mM Tris-Cl (pH 7.6) and incubated with RNaseA.
The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, nature). The amplified DNA was digested with Dnase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.


title: WCE fraction of wild type cells treated with alpha-factor, input

description:
WCE fraction of wild type cells treated with alpha-factor (chromosome III, IV, V, and the right arm of chromosome VI)
WCE fraction used for the nomalization of ChIP fraction
Baseline for wild type, rad53, and rad53 siz2 mutant treated with alpha-factor

treatment_protocol:
Early log phase culture was harvested and resuspended in YPAD medium at 1x10e7. Then, cells were treated with 15 ug/ml alpha-factor.
1x10e9 cells were fixed in 1% formaldehyde for 10 min at room temperature and then treated with 125 mM glycine for 5 min at room temperature. The cells were washed with 20 ml of ice-cold TBS twice, freezed with liquid nitrogen, and stored at -80C.

value: Wild type expressing Rad52-13myc

value: arrested in G1 with alpha-factor


title: rad53 mutant treated with alpha factor, IP fraction

description:
Distribution of Rad52-myc on chromosome III, IV, V, and the right arm of chromosome VI (rad53 mutant treated with alpha factor)
IP fraction used for the mapping of Rad52-13myc on chromosomes
Used baseline: WCE fraction of wild type cells treated with alpha-factor

value: rad53 mutant expressing Rad52-13myc


title: WCE fraction of rad53 mutant treated with HU, input

description:
WCE fraction of rad53 mutant treated with HU (chromosome III, IV, V, and the right arm of chromosome VI)
WCE fraction used for the nomalization of ChIP fraction
Baseline for rad53 mutant treated with HU


title: YUSTE, metastatic melanoma, rep1

city: New Haven

first: Ruth

last: Halaban

state: CT

address: 15 York St.

department: Dermatology

institute: Yale University

description: Genome-wide gene expression of YUSTE metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

hyb_protocol: Standard Nimblegen Protocol, performed by Nimblegen.

data_processing: The qspline normalization method (Workman et al., 2002) was used to normalize a set of single channels hybridization derived from a two channel platform. In particular, the qspline implementation available in the affy Bioconductor was used (http://www.bioconductor.org/).

source_name: metastatic melanoma

label_protocol: Standard Nimblegen Protocol.

growth_protocol: Melanoma cells from metastatic melanoma were excised from tumor samples and used during the third passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

extract_protocol: Approximately 20–30 million cells (normal human melanocytes and melanoma cells/each) were used for mRNA extraction. High-quality total RNA was prepared with the TRIzol reagent (Invitrogen Life Technologies, Inc., Invitrogen Corp., Carlsbad, CA). The quality of RNA products was determined visually by 1% denaturing agarose gel, and RNA concentration was measured using a spectrophotometer. Poly(A) mRNA was further isolated from 150-300 µg total RNA/sample using the PolyATtract mRNA isolation system IV (Pro-mega, Madison, WI) following the manufacturer’s instructions, and reversed transcribed to double stranded cDNA. This additional step is required to eliminate the melanin present in the total RNA preparation that suppresses PCR hybridization reactions.

tag: Gender

tag: Age

value: 66 year


title: rad53 siz2 mutant treated with alpha factor, IP fraction

description:
Distribution of Rad52-myc on chromosome III, IV, V, and the right arm of chromosome VI (rad53 siz2 mutant treated with alpha factor)
IP fraction used for the mapping of Rad52-13myc on chromosomes
Used baseline: WCE fraction of wild type cells treated with alpha-factor

tag: strain


title: WCE fraction of wild type cells treated with HU, input

description:
WCE fraction of wild type cells treated with HU (chromosome III, IV, V, and the right arm of chromosome VI)
WCE fraction used for the nomalization of ChIP fraction
Baseline for wild type treated with HU


title: wild type cells treated with HU, IP fraction

description:
Distribution of Rad52-myc on chromosome III, IV, V, and the right arm of chromosome VI (wild type cells treated with HU)
IP fraction used for the mapping of Rad52-13myc on chromosomes
Used baseline: WCE fraction of wild type cells treated with HU

value: Wild type strain expressing Rad52-13myc


title: YURIF, soft tissue metastatic melanoma, rep3

description: Genome-wide gene expression of YURIF soft tissue metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

scan_protocol: Standard Nimblegen Protocol, performed by Nimblegen.

source_name: soft tissue metastasis

growth_protocol: Melanoma cells from soft tissue metastasis were excised from tumor samples and used during the 1st passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

value: male

value: 53 year

tag: Tissue

value: soft tissue


title: YUSTE, metastatic melanoma, rep3

description: Genome-wide gene expression of YULAC metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

growth_protocol: Melanoma cells from metastatic melanoma were excised from tumor samples and used during the 11th passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

value: female


title: rad53 mutant treated with HU, IP fraction

description:
Distribution of Rad52-myc on chromosome III, IV, V, and the right arm of chromosome VI (rad53 mutant treated with HU)
IP fraction used for the mapping of Rad52-13myc on chromosomes
Used baseline: WCE fraction of rad53 mutant treated with HU


title: YURIF, soft tissue metastatic melanoma, rep4


title: YURIF, soft tissue metastatic melanoma, rep2


title: YULAC, metastatic melanoma, rep2


title: YUSTE, metastatic melanoma, rep2


title: wild type cells treated with alpha factor, IP fraction

description:
Distribution of Rad52-myc on chromosome III, IV, V, and the right arm of chromosome VI (wild type cells treated with alpha factor)
IP fraction used for the mapping of Rad52-13myc on chromosomes
Used baseline: WCE fraction of wild type cells treated with alpha-factor


title: YULAC, metastatic melanoma, rep1


title: YUSIT1, metastatic melanoma, rep4

description: Genome-wide gene expression of YUSIT1 metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

growth_protocol: Melanoma cells from metastatic melanoma were excised from tumor samples and used during the second passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

value: 67 year


title: Small Cell Lung Cancer Primary Tumor 95-2889 (95-2889)

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: No additional description available for sample: 95-2889

hyb_protocol: Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133A 2.0 Array. The array was then washed and stained with streptavidin?phycoerythrin (Molecular Probes) using the GeneChip Fluidics Workstation 450 (Affymetrix).

scan_protocol: The gene chip was then scanned using a confocal laser scanner (Affymetrix GeneArray Scanner 3000)

data_processing: The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.

source_name: Small Cell Lung Cancer Primary Tumor: 95-2889

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 to 5 microg total RNA. In brief, double-stranded cDNA synthesis was prepared from 2.5 to 5 µg of total RNA (SuperScript double-stranded cDNA synthesis kit; Invitrogen). After purification (QIAquick, Qiagen AG), the cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High yield T7 DNA transcription kit, ENZO Life Sciences). The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG).

extract_protocol: Total RNA was purified using RNAzol (Invitrogen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 7.5 were profiled.

tag: sample

tag: type

value: tissue

tag: disease state

value: Small Cell Lung Cancer


title: Small Cell Lung Cancer Primary Tumor 96-15625 (96-15625)

description: No additional description available for sample: 96-15625

source_name: Small Cell Lung Cancer Primary Tumor: 96-15625


title: YURIF, soft tissue metastatic melanoma, rep1


title: YUSIT1, metastatic melanoma, rep3

description: Genome-wide gene expression of YUSIT metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.


title: Small Cell Lung Cancer Primary Tumor 89-18331 (89-18331)

description: No additional description available for sample: 89-18331

source_name: Small Cell Lung Cancer Primary Tumor: 89-18331


title: YUSIT1, metastatic melanoma, rep2


title: Small Cell Lung Cancer Primary Tumor 94-12260 (94-12260)

description: No additional description available for sample: 94-12260

source_name: Small Cell Lung Cancer Primary Tumor: 94-12260


title: YUSAC2, lymph node metastatic melanoma, rep5

description: Genome-wide gene expression of YUSAC2 lymph node metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

source_name: lymph node metastasis

growth_protocol: Melanoma cells from lymph node metastasis were excised from tumor samples and used during the second passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

value: 57 year

value: lymph node


title: YUGEN8, brain metastatic melanoma, rep2

description: Genome-wide gene expression of YUGEN8 brain metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

source_name: brain metastasis

growth_protocol: Melanoma cells from brain metastasis were excised from tumor samples and used during the fifth passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

tag: Age:44 year

value: brain


title: HRG 36h00m rep1

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN RCAI

description: From early to late gene expression (10min to 72hour) induced by growth hormone stimulation.

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: The data were analyzed with GeneChip Operating System (GCOS) (ver.1.2) using Affymetrix default analysis settings and global scaling as normalization method. The Single-Array Expression Analysis function was used and the trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: breast epithelial cell, adherent, HRG, 36h

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: Cell line

value: MCF-7 (Obtained from ATCC (American Type Culture Collection)), Organ:mammary gland; breast, Cell type:epithelial, Disease:adenocarcinoma, Derived from metastatic site:pleural effusion, Age:69 years adult, Gender:female, Ethnicity:Caucasian


title: YUGEN8, brain metastatic melanoma, rep1

source_name: brain metastatic melanoma

value: 44 year


title: YUSIT1, metastatic melanoma, rep1


title: YUMAC, soft tissue metastatic melanoma, rep6

description: Genome-wide gene expression of YUMAC soft tissue metastatic melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

growth_protocol: Melanoma cells from soft tissue metastatic lesion were excised from tumor samples and used during the tenth passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

value: 68 year


title: HRG 72h00m rep2

source_name: breast epithelial cell, adherent, HRG, 72h


title: YUMAC, soft tissue metastatic melanoma, rep7


title: YUMAC, soft tissue metastatic melanoma, rep5


title: HRG 36h00m rep2


title: HRG 24h00m rep2

source_name: breast epithelial cell, adherent, HRG, 24h


title: HRG 72h00m rep1


title: HRG 24h00m rep1


title: YUMAC, soft tissue metastatic melanoma, rep4


title: YUMAC, soft tissue metastatic melanoma, rep3

growth_protocol: Melanoma cells from soft tissue metastatic lesion were excised from tumor samples and used during the 10th passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.


title: WW165, primary melanoma, rep3

description: Genome-wide gene expression of WW165 primary melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

source_name: primary melanoma

growth_protocol: Melanoma cells from primary melanoma were excised from tumor samples and used during the fifth passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

value: 62 year


title: HRG 12h00m rep2

source_name: breast epithelial cell, adherent, HRG, 12h


title: HRG 48h00m rep2

source_name: breast epithelial cell, adherent, HRG, 48h


title: YUMAC, soft tissue metastatic melanoma, rep2


title: HRG 12h00m rep1


title: HRG 08h00m rep2

source_name: breast epithelial cell, adherent, HRG, 8h


title: WW165, primary melanoma, rep2


title: HRG 48h00m rep1


title: WW165, primary melanoma, rep1


title: HRG 06h00m rep1

source_name: breast epithelial cell, adherent, HRG, 6h


title: HRG 06h00m rep2


title: HRG 08h00m rep1


title: Newborn normal melanocytes, rep2

description: Genome-wide gene expression of newborn normal melanocytes is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.

source_name: newborn foreskin

growth_protocol: Normal human melanocytes isolated from newborn foreskins were used during the first passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.

value: 0 year

value: foreskin


title: HRG 04h00m rep2

source_name: breast epithelial cell, adherent, HRG, 4h


title: YUSAC2, lymph node metastatic melanoma, rep3

growth_protocol: Melanoma cells from lymph node metastasis were excised from tumor samples and were used at the second passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.


title: HRG 03h00m rep2

source_name: breast epithelial cell, adherent, HRG, 3h


title: Newborn normal melanocytes, rep3


title: HRG 04h00m rep1


title: YUSAC2, lymph node metastatic melanoma, rep2


title: HRG 02h00m rep1

source_name: breast epithelial cell, adherent, HRG, 2h


title: HRG 03h00m rep1


title: YUSAC2, lymph node metastatic melanoma, rep 4


title: YUMAC, soft tissue metastatic melanoma, rep1

source_name: soft tissue metastasis

growth_protocol: Melanoma cells from soft tissue metastasis were excised from tumor samples and were used at the 10th passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.


title: YUSAC2, lymph node metastatic melanoma, rep1


title: mes-2 embryo, 8E stage, Replicate 3

city: Salt Lake City

last: Mango

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description: total RNA from a single embryos

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing:
TIF image files were processed with Agilent Feature Extraction Software version 9.5.1.
Non-uniform features were discarded and features with the same probe were averaged. Mean spot intensity was log (base 2) transformed and quantile normalized within groups. Group medians were adjusted to be equal.

organism: Caenorhabditis elegans

source_name: Cy3_WT mix embryos; Cy5_mes-2 8E single embryo

label_protocol: PCR-amplified DNA samples (2-3 µg) derived from chromatin immunoprecipitation reactions were labeled using the Agilent Genomic DNA Labeling Kit PLUS.  The labeling kit uses random primers and the exo-Klenow fragment to label DNA through incorporation of fluorescently labeled nucleotides (Cy3-dUTP or Cy5-dUTP).  Following termination of the labeling reaction, fluorescently labeled DNA molecules were purified by isopropanol precipitation.  Precipitated pellets were dried and then rehydrated in distilled water.  The concentration of purified samples was determined using a NanoDrop ND-1000 spectrophotometer.  A fraction of the labeled DNA (100 ng) was run on an Agilent BioAnalyzer to validate the size distribution of the labeled DNA molecules.

growth_protocol: 2-cell embryos were collected from wild-type or mes-2 mothers and incubated at 20°C for 75 min. (2E), 120 min. (4E), 3h. (8E).

extract_protocol: cDNA from individual embryos was isolated as described (Robertson et al., 2004). Briefly, individual embryos were placed in 0.5 $B&L (Bl of cDNA 1st-strand buffer (Robertson et al., 2004), squashed with a small piece of coverslip and immediately frozen on dry ice. Upon thawing, 4 $B&L (Bl of 1st -strand buffer was added to each embryo. After heating to 65 °C (BC for 90 s, the tube was cooled to 45 °C (BC and reverse transcription initiated with the addition of 0.5 $B&L (Bl Superscript III. After 60 min, the reaction was terminated by heating to 70 °C (BC for 15 min, 0.5 $B&L (Bl RNAse H was added and RNA digested at 37 °C (BC for 20 min. The cDNA strands were polyA tailed by the addition of 5 $B&L (Bl of 2 $B!_ (B TdT buffer containing dATP, and terminal deoxynucleotidyl transferase, and incubated at 37 °C (BC for 15 min. Tailing was stopped by heating to 65 °C (BC for 10 min. 40 °C (Bl of PCR buffer was added to each tube followed by 50 cycles of PCR amplification. This primary RT-PCR amplification product could then be reamplified as needed to generate more total cDNA.

tag: strain (cy3)

tag: strain (cy5)


title: Newborn normal melanocytes, rep1


title: HRG 01h30m rep2

source_name: breast epithelial cell, adherent, HRG, 1h30min


title: HRG 01h30m rep1


title: HRG 01h00m rep2

source_name: breast epithelial cell, adherent, HRG, 1h


title: HRG 02h00m rep2


title: mes-2 embryo, 8E stage, Replicate 2

description: total RNA from a single embryos


title: mes-2 embryo, 8E stage, Replicate 1

description: total RNA from a single embryos


title: mes-2 embryo, 4E stage, Replicate 3

description: total RNA from a single embryos

source_name: Cy3_WT mix embryos; Cy5_mes-2 4E single embryo


title: HRG 00h45m rep2

source_name: breast epithelial cell, adherent, HRG, 45min


title: mes-2 embryo, 4E stage, Replicate 2

description: total RNA from a single embryos


title: HRG 01h00m rep1


title: HRG 00h30m rep2

source_name: breast epithelial cell, adherent, HRG, 30min


title: HRG 00h45m rep1


title: mes-2 embryo, 4E stage, Replicate 1

description: total RNA from a single embryos


title: HRG 00h20m rep2

source_name: breast epithelial cell, adherent, HRG, 20min


title: HRG 00h15m rep2

source_name: breast epithelial cell, adherent, HRG, 15min


title: Wild type embryo, 8E stage, Replicate 3

description: total RNA from a single embryos

source_name: Cy3_WT mix embryos; Cy5_WT 8E single embryo


title: HRG 00h10m rep2

source_name: breast epithelial cell, adherent, HRG, 10min


title: HRG 00h30m rep1


title: mes-2 embryo, 2E stage, Replicate 3

description: total RNA from a single embryos

source_name: Cy3_WT mix embryos; Cy5_mes-2 2E single embryo


title: Wild type embryo, 8E stage, Replicate 1

description: total RNA from a single embryos


title: Wild type embryo, 8E stage, Replicate 2

description: total RNA from a single embryos


title: Wild type embryo, 4E stage, Replicate 2

description: total RNA from a single embryos

source_name: Cy3_WT mix embryos; Cy5_WT 4E single embryo


title: HRG 00h15m rep1


title: mes-2 embryo, 2E stage, Replicate 1

description: total RNA from a single embryos


title: Wild type embryo, 4E stage, Replicate 1

description: total RNA from a single embryos


title: HRG 00h10m rep1


title: HRG 00h20m rep1


title: Wild type embryo, 4E stage, Replicate 3

description: total RNA from a single embryos


title: Wild type embryo, 2E stage, Replicate 3

description: total RNA from a single embryos

source_name: Cy3_WT mix embryos; Cy5_WT 2E single embryo


title: EGF 72h00m rep2

source_name: breast epithelial cell, adherent, EGF, 72h


title: Wild type embryo, 2E stage, Replicate 1

description: total RNA from a single embryos


title: EGF 72h00m rep1


title: Wild type embryo, 2E stage, Replicate 2

description: total RNA from a single embryos


title: EGF 48h00m rep2

source_name: breast epithelial cell, adherent, EGF, 48h


title: Wild type embryo, 2-cell stage, Replicate 1

description: total RNA from a single embryos

source_name: Cy3_WT mix embryos; Cy5_WT 2-cell single embryo


title: EGF 48h00m rep1


title: EGF 36h00m rep2

source_name: breast epithelial cell, adherent, EGF, 36h


title: EGF 24h00m rep2

source_name: breast epithelial cell, adherent, EGF, 24h


title: EGF 08h00m rep2

source_name: breast epithelial cell, adherent, EGF, 8h


title: EGF 12h00m rep2

source_name: breast epithelial cell, adherent, EGF, 12h


title: EGF 08h00m rep1


title: EGF 06h00m rep2

source_name: breast epithelial cell, adherent, EGF, 6h


title: EGF 04h00m rep2

source_name: breast epithelial cell, adherent, EGF, 4h


title: EGF 12h00m rep1


title: EGF 06h00m rep1


title: EGF 24h00m rep1


title: EGF 03h00m rep2

source_name: breast epithelial cell, adherent, EGF, 3h


title: EGF 02h00m rep2

source_name: breast epithelial cell, adherent, EGF, 2h


title: EGF 02h00m rep1


title: EGF 01h30m rep1

source_name: breast epithelial cell, adherent, EGF, 1h30min


title: EGF 03h00m rep1


title: EGF 00h45m rep2

source_name: breast epithelial cell, adherent, EGF, 45min


title: EGF 04h00m rep1


title: EGF 01h30m rep2


title: EGF 00h45m rep1


title: EGF 00h30m rep2

source_name: breast epithelial cell, adherent, EGF, 30min


title: EGF 00h30m rep1


title: EGF 36h00m rep1


title: EGF 00h10m rep2

source_name: breast epithelial cell, adherent, EGF, 10min


title: EGF 00h15m rep2

source_name: breast epithelial cell, adherent, EGF, 15min


title: EGF 01h00m rep1

source_name: breast epithelial cell, adherent, EGF, 1h


title: EGF 00h20m rep2

source_name: breast epithelial cell, adherent, EGF, 20min


title: EGF 00h15m rep1


title: EGF 00h20m rep1


title: Control

source_name: breast epithelial cell, adherent, Control


title: EGF 00h10m rep1


title: PA-Isolate M26-2

city: Munich

first: michael

last: Hogardt

state: Bavaria

address: Marchioninistreet 17

department: Bacteriology

country: Germany

institute: Max von Pettenkofer-Institut

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M23

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

organism: Pseudomonas aeruginosa

source_name: liquid culture

label_protocol: Affymetrix prokaryotic standard protocol

growth_protocol: Luria Bertani/300rpm/OD600nm ~3.5

extract_protocol: TRIzol (Invitrogen) according to the manufacturer's instructions.

tag: PA-Isolate M26-2 from patient M

tag: mutator

tag: Isolate recovered on Sep 2001


title: EGF 01h00m rep2


title: PA-Isolate M26-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M24

tag: PA-Isolate M26-3 from patient M


title: PA-Isolate M25-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M21

tag: PA-Isolate M25-3 from patient M


title: PA-Isolate M25-2

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M20

tag: PA-Isolate M25-2 from patient M


title: PA-Isolate M25-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M19

tag: PA-Isolate M25-1 from patient M


title: PA-Isolate M26-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M22

tag: PA-Isolate M26-1 from patient M


title: PA-Isolate M23-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M18

tag: PA-Isolate M23-3 from patient M

tag: non-mutator

tag: Isolate recovered on Jun 2001


title: PA-Isolate M23-2

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M17

tag: PA-Isolate M23-2 from patient M


title: PA-Isolate M23-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M16

tag: PA-Isolate M23-1 from patient M


title: PA-Isolate M22-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M15

tag: PA-Isolate M22-3 from patient M

tag: Isolate recovered on May 2001


title: PA-Isolate M22-2

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M14

tag: PA-Isolate M22-2 from patient M


title: PA-Isolate M22-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M13

tag: PA-Isolate M22-1 from patient M


title: PA-Isolate M13-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M12

tag: PA-Isolate M13-3 from patient M

tag: Isolate recovered on Oct 1999


title: PA-Isolate M13-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M10

tag: PA-Isolate M13-1 from patient M

tag: mutator


title: PA-Isolate M13-2

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M11

tag: PA-Isolate M13-2 from patient M


title: PA-Isolate M11-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M7

tag: PA-Isolate M11-1 from patient M


title: PA-Isolate M11-2

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M8

tag: PA-Isolate M11-2 from patient M


title: Earliest PA-Isolate M1-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M3

tag: Earliest PA-Isolate M1-3 from patient M

tag: Isolate recovered on Feb 1998


title: PA-Isolate M9-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M4

tag: PA-Isolate M9-1 from patient M

tag: non-mutator

tag: Isolate recovered on Sep 1998


title: PA-Isolate M9-2

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M5

tag: PA-Isolate M9-2 from patient M


title: PA-Isolate M11-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M9

tag: PA-Isolate M11-3 from patient M


title: PA-Isolate M9-3

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M6

tag: PA-Isolate M9-3 from patient M


title: Earliest PA-Isolate M1-2

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M2

tag: Earliest PA-Isolate M1-2 from patient M


title: Wild type embryo, 2-cell stage, Replicate 3

description: total RNA from a single embryos

source_name: Cy3_WT mix embryos; Cy5_WT 2-cell single embryo

tag: strain (cy3)

tag: strain (cy5)


title: Wild type embryo, 2-cell stage, Replicate 2

description: total RNA from a single embryos


title: Earliest PA-Isolate M1-1

description: Gene expression data from P. aeruginosa cystic fibrosis isolate M1

tag: Earliest PA-Isolate M1-1 from patient M


title: Mouse (Coco/KO)_soleus_11months_rep3

status: Public on May 25 2009

city: Nedlands

first: Kristen

middle: Jean

last: Nowak

address: WAIMR, B Block, QEII Medical Centre

department: Centre for Medical Research

country: Australia

institute: University of Western Australia/WA Institute for Medical Research

description: 4068846025 D

hyb_protocol: 1.5 micrograms of cRNA per sample was hybridized onto the array for 17 hours at 58 degrees celcius.

scan_protocol: The chip was scanned using an Illumina BeadScan

data_processing: The background was substracted using  Illumina BeadStudio software.  Data normalization (as per Lin, Du, Huber & Kibbe (2008), Nucleic Acids Res 36, e11) and differential gene expression analysis (Bioconductor lumi and Limma software packages) was performed by Creative Biomics (http://www.creative-biomics.com/)

source_name: soleus, male, 11months

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion) as per manufacturer's instructions

extract_protocol: Whole soleus muscles were excised from recently euthanased mice before snap freezing in liquid nitrogen.  Each soleus was cut into cryostat sections (10 microns) which were kept frozen in a dry ice-chilled tube until the addition of 1ml of TriReagent (Sigma). The TriReagent protocol was followed, except that instead of resuspending the RNA pellet into water as a final step, the pellet was resuspended into 600 microlitres of RLT buffer from the RNeasyPlus kit (Qiagen), and then the manufacturer's instructions for this kit followed from there.

treatment_protocol: Male, 11 month old mice (either wild-type or Coco/KO), were sacrificed, and then the soleus muscles excised and snap frozen in liquid nitrogen.

tag: Mouse strain

value: Coco/KO (CBB6F1xFVB/n), Sex:Male, Muscle:soleus, Age:11 months


title: Mouse (Wildtype)_soleus_11months_rep3

description: 4068846025 F

tag: mouse strain

value: Wildtype (CBB6F1xFVB/n), Sex:Male, Muscle:soleus, Age:11 months


title: Mouse (Wildtype)_soleus_11months_rep2

description: 4068846025 E


title: Infected Vero cells@34C rep 5

status: Public on May 23 2009

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Infected Vero cells@34C rep 5

hyb_protocol: ~1ug label and fragmented applied for 16hrs 40OC

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7GPlus Scanner.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Rickettsia rickettsii

source_name: Infected Vero cells@34C rep 5

label_protocol: Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix) was used to label the 3′ termini of the fragmented cDNA products. Labeled cDNA (1 µg) was hybridized to custom Affymetrix GeneChips

growth_protocol: R. rickettsii R strain was propagated in Vero cells with M199 medium or ISE6 tick cells (Munderloh et al., 1999) with L-15B medium and purified by Renografin density gradient centrifugation (Weiss et al., 1975). To determine the growth rate of R. rickettsii R strain grown at different temperatures, R. rickettsii was grown on monolayers of either ISE6 or Vero cells in T25 flasks (MOI of 0.025). For the growth rates of R. rickettsii R strain under limiting iron conditions, rickettsiae were grown on monolayers of Vero cells (MOI of 0.025) in 6 well plates with 0, 100, 200 and 500 μM concentrations of deferozamine mesylate (Sigma). To restore growth in the presence of 200 or 500 μM deferozamine mesylate, iron saturated holotransferrin (Sigma) was included at concentrations of 12 and 24 mg/ml respectively. At the appropriate times after infection, the medium was removed and 1 ml of K36 (0.1 M KCl, 0.015 M NaCl, 0.05 M K2HPO4, 0.05 M KH2PO4, pH 7.0) was added. The monolayer was removed by scraping and the host cells were lysed by bead beating 2X for 4 seconds with (1 mm) glass beads. The cell suspension was then frozen at -80°C until plaque assays were performed. Plaque assays were performed as 17 previously described (Cory et al., 1974). All growth curves are representative of multiple experiments and each point is an average of at least two replicate platings.

extract_protocol: Total RNA from each sample was stabilized with RNAProtect (Qiagen), extracted and purified using the 96-well plate RNAeasy kit (Qiagen) with slight modifications. RNA samples were treated with DNA-free DNase I (Ambion) and the quality of DNA-free RNAs were monitored on Agilent RNA Pico II LabChips (Agilent Technologies). Additionally, possible DNA contamination was tested by qPCR (see below). 10 mg of total RNA from each sample was reverse-transcribed to cDNA using random hexamer primers (Invitrogen) and SuperScript III reverse transcriptase (Invitrogen). RNA was removed and cDNA was purified using a QiaQuick 96 PCR purification kit (Qiagen), quantified and fragmented with DNase I (Roche)

treatment_protocol: To investigate the transcriptional response of R. rickettsii exposed to limiting iron conditions, monolayers of Vero cells in T25 tissue culture flasks were infected with R. rickettsii R strain at an MOI of 0.025. To mimic iron limitation R. rickettsii were grown for three days at 34°C at which time 200 μM of deferozamine mesylate was added to the flasks and incubated for 24 hours. Total RNA was extracted by removing the growth media and adding 1 ml of Trizol (Invitrogen) to thee T25 tissue culture flasks grown for three days and to three T25 tissue culture flasks exposed to iron limiting conditions for 24 hrs. To examine gene expression at different growth temperatures monolayers of Vero or ISE6 cells in T25 tissue culture flasks were infected with R. rickettsii R strain at an MOI of 0.025. Total RNA was extracted as above from five T25 tissue culture flasks grown at 37°C or 34°C for two and three days after infection and total RNA from five T25 tissue culture flasks grown at 25°C or 22°C for six and eight days following infection.  To study cold shock response in R. rickettsii 15 T25 flasks were infected with an MOI of 0.025 and incubated at 34°C for three days. After three days of growth five flasks were removed for isolation of total RNA and the remainder were shifted to 4°C for 2 hrs. After 2 hrs, total RNA from 5 flasks was extracted and the remaining five flasks were shifted back to 34°C for 2 hrs before total RNA was extracted. In a separate experiment six T25 tissue culture flasks were infected with an MOI of 0.025 and grown for three days at 34°C. As above total RNA was extracted from three T25 tissue culture 18 flasks on day three after infection and three T25 tissue culture flasks were moved to 4°C for 24 hrs before extraction.  For iron limitation, growth temperature and cold shock plaque forming units (PFUs) were determined to ensure equal numbers of rickettsiae were being compared in each experiment. To determine non-specific background from ISE6 and Vero RNA, RNA was harvested from uninfected samples and hybridized to the microarrays. These experiments showed a false positive rate of 2 to 5%. These genes were removed from the final analysis.

tag: genotype

value: R strain


title: Infected Vero cells@34C rep 4

description: Gene expression data from_Infected Vero cells@34C rep 4

source_name: Infected Vero cells@34C rep 4


title: Mouse (Coco/KO)_soleus_11months_rep1

description: 4068846025 A


title: Mouse (Wildtype)_soleus_11months_rep1

description: 4068846025 B


title: Infected Vero cells@34C rep 3

description: Gene expression data from_Infected Vero cells@34C rep 3

source_name: Infected Vero cells@34C rep 3


title: Infected Vero cells@34C rep 2

description: Gene expression data from_Infected Vero cells@34C rep 2

source_name: Infected Vero cells@34C rep 2


title: Mouse (Coco/KO)_soleus_11months_rep2

description: 4068846025 C


title: YUSAC2, lymph node metastatic melanoma

description: Genome-wide promoter methylation status of YUSAC lymph node metastatic melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

data_processing: Nimblegen C4226-00-01 genome-wide promoter tiling array based on the hg18 genome release was used. It contains 390,000 probes with an average length of 60nt tiled along gene upstream regions each 110 bp. Within (Loess based) and between (Quantile based) normalization methods available in the Limma Bioconductor library  as standard methods for two-channel microarrays are applied. The probe-level log ratio was determined as the log2 of the cy3/cy5 channels and used as a measure of MeDIP enrichment.

source_name: lymph node methastasis (MeDIP DNA)

label_protocol: The MeDIP assay was performed as described . Briefly, genomic DNA was extracted by DNeasy Blood & Tissue Kit (QIAGEN), sheared into 300-1,200 bp fragments by sonication, and aliquots (10 µg) were incubated with 20 µl anti-5-methylcytidine mAb (Eurogentec), for 12 hr at 4ºC. Antibody bound DNA was precipitated with 50 l Dynabeads (M-280 sheep antibodies to mouse IgG, Dynal Biotech) at 4ºC for 2hr, on a rotating wheel. Bound DNA was eluted two times with 200 ul TE containing 1.0% and 0.67% SDS, respectively, and DNA was purified by standard proteinase K/phenol-chloroform procedure. The DNA samples from eluted fractions and sonicated input DNA were differentially labeled with fluorescent dyes (Cy3 and Cy5, respectively) and hybridized to the genomic promoter tiling arrays.

growth_protocol: Normal human melanocytes were isolated from newborn foreskins and adult skins and used during the first passage in culture. The cells were grown in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements as described . Melanoma tumors were resected to benefit the patients and were collected with participants’ informed signed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol. A portion of the tumor was snap-frozen in liquid nitrogen and the other was dissociated and cultured in basal medium (metastatic cells) or in medium supplemented with 0.1 mM 3-isobutyl-1-methyl xanthin (Sigma) (primary melanoma), a supplement required for their proliferation. Melanoma cells from primary and metastatic lesions were from short-term cultures, i.e., passage 1-15.

extract_protocol: DNeasy Blood & Tissue Kit (QIAGEN)

tag: Gender

value: male

tag: Age

tag: Tissue

source_name: lymph node methastasis (input DNA)


title: YUSIT1, metastatic melanoma

description: Genome-wide promoter methylation status of YUSIT1 metastatic melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

source_name: metastatic melanoma (MeDIP DNA)

source_name: metastatic melanoma (input DNA)


title: Infected Vero cells@34C rep 1

description: Gene expression data from_Infected Vero cells@34C rep 1

source_name: Infected Vero cells@34C rep 1


title: WW165, primary melanoma

description: Genome-wide promoter methylation status of WW165 primary melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

source_name: primary melanoma (MeDIP DNA)

value: female

value: primary melanoma

source_name: primary melanoma (input DNA)


title: Infected Vero cells@25C rep 4

description: Gene expression data from_Infected Vero cells@25C rep 4

source_name: Infected Vero cells@25C rep 4


title: YUMAC, soft tissue metastatic melanoma

description: Genome-wide promoter methylation status of YUMAC soft tissue metastatic melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

source_name: soft tissue metastasis (MeDIP DNA)

label_protocol: The MeDIP assay was performed as described . Briefly, genomic DNA was extracted by DNeasy Blood & Tissue Kit (QIAGEN), sheared into 300-1,200 bp fragments by sonication, and aliquots (10 µg) were incubated with 20 µl anti-5-methylcytidine mAb (Eurogentec), for 12 hr at 4ºC. Antibody bound DNA was precipitated with 50 l Dynabeads (M-280 sheep antibodies to mouse IgG, Dynal Biotech) at 4ºC for 2hr, on a rotating wheel. Bound DNA was eluted two times with 200 l TE containing 1.0% and 0.67% SDS, respectively, and DNA was purified by standard proteinase K/phenol-chloroform procedure. The DNA samples from eluted fractions and sonicated input DNA were differentially labeled with fluorescent dyes (Cy3 and Cy5, respectively) and hybridized to the genomic promoter tiling arrays.

value: soft tissue

source_name: soft tissue metastasis (input DNA)


title: Infected Vero cells@25C rep 5

description: Gene expression data from_Infected Vero cells@25C rep 5

source_name: Infected Vero cells@25C rep 5


title: Non-Infected Vero cells@345C rep 3

description: Gene expression data from_Non-Infected Vero cells@345C rep 3

source_name: Non-Infected Vero cells@345C rep 3


title: Non-Infected Vero cells@345C rep 5

description: Gene expression data from_Non-Infected Vero cells@345C rep 5

source_name: Non-Infected Vero cells@345C rep 5


title: YUSTE, metastatic melanoma

description: Genome-wide promoter methylation status of YUSTE metastatic melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

value: 66 year


title: Infected Vero cells@25C rep 1

description: Gene expression data from_Infected Vero cells@25C rep 1

source_name: Infected Vero cells@25C rep 1


title: Infected Vero cells@25C rep 3

description: Gene expression data from_Infected Vero cells@25C rep 3

source_name: Infected Vero cells@25C rep 3


title: Infected Vero cells@25C rep 2

description: Gene expression data from_Infected Vero cells@25C rep 2

source_name: Infected Vero cells@25C rep 2


title: Non-Infected Vero cells@345C rep 4

description: Gene expression data from_Non-Infected Vero cells@345C rep 4

source_name: Non-Infected Vero cells@345C rep 4


title: Non-Infected Vero cells@345C rep 1

description: Gene expression data from_Non-Infected Vero cells@345C rep 1

source_name: Non-Infected Vero cells@345C rep 1


title: Non-Infected Vero cells@345C rep 2

description: Gene expression data from_Non-Infected Vero cells@345C rep 2

source_name: Non-Infected Vero cells@345C rep 2


title: YUGEN8, brain metastatic melanoma

description: Genome-wide promoter methylation status of YUGEN8 brain metastasis melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

source_name: brain metastatic melanoma (MeDIP DNA)

source_name: brain metastatic melanoma (input DNA)


title: YULAC, metastatic melanoma

description: Genome-wide promoter methylation status of YULAC metastatic melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

source_name: metastatic melanoma (MeDIP DNA)

source_name: metastatic melanoma (input DNA)